[Chimera-users] atoms/residues within a certain distance of another structure

[Eric Pettersen]

On Jun 12, 2007, at 12:25 AM, Kenward Vaughan wrote:

> On Mon, 2007-06-11 at 19:15 -0700, Terry Nelson wrote:
>> Hi,
>>      1. I was wondering if Chimera has the option of finding for
>>         instance : "residues within 5 Angstrom of a bound protein
>>         inhibitor" or "residues within 3Ang. of solvent molecules",

>
> 	select <description of atoms/residues> z<5.0     # or zr<5.0
> or
> 	select <description of atoms/residues> za<5.0

The only thing I would add is that Chimera guesstimates what parts of  
a system are ligand, solvent, etc., so "<description of atoms/ 
residues>" in the above may simply be "ligand" or "solvent".  You can  
see what Chimera has classified as ligand/solvent with "select  
ligand" or "sel solvent".

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu